rs6938674

Variant names:

• chr6-31440227-T-C
• rs6938674
• ENST00000673857.1:n.63-22896T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.63-22896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 151,922 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.033 (142 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 7 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288587	ENST00000673857.1		n.63-22896T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0333 AC: 5059 AN: 151804 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.0398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0334 AC: 5079 AN: 151922 Hom.: 142 Cov.: 31 AF XY: 0.0332 AC XY: 2467 AN XY: 74294

African (AFR) AF: 0.0303 AC: 1251 AN: 41352

American (AMR) AF: 0.0280 AC: 426 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0338 AC: 117 AN: 3466

East Asian (EAS) AF: 0.0803 AC: 415 AN: 5168

South Asian (SAS) AF: 0.0266 AC: 128 AN: 4812

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0351 AC: 2387 AN: 67998

Other (OTH) AF: 0.0465 AC: 98 AN: 2106

Alfa AF: 0.0351 Hom.: 349

Bravo AF: 0.0331

Asia WGS AF: 0.0510 AC: 178 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.2
DANN	Benign	0.77
PhyloP100		-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6938674;

hg19: chr6-31408004;